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Genome Sequence of Bacillus anthracis Strain Tangail-1 from Bangladesh Farzana Islam Rume,a Markus Antwerpen,b Peter Braun,b Paritosh Kumar Biswas,c Mahmuda Yasmin,a Gregor Grass,b Chowdhury Rafiqul Ahsan,a Matthias Hanczarukb Department of Microbiology, University of Dhaka, Dhaka, Bangladesha; Bundeswehr Institute of Microbiology, Munich, Germanyb; Department of Microbiology and Veterinary Public Health, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladeshc
Soil was collected in July 2013 at a site where a cow infected with anthrax had been the month before. Selective culturing yielded Bacillus anthracis strain Tangail-1. Here, we report the draft genome sequence of this Bacillus anthracis isolate that belongs to the canonical A.Br.001/002 clade. Received 3 June 2016 Accepted 6 June 2016 Published 28 July 2016 Citation Rume FI, Antwerpen M, Braun P, Biswas PK, Yasmin M, Grass G, Ahsan CR, Hanczaruk M. 2016. Genome sequence of Bacillus anthracis strain Tangail-1 from Bangladesh. Genome Announc 4(4):e00748-16. doi:10.1128/genomeA.00748-16. Copyright © 2016 Rume et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Markus Antwerpen,
[email protected].
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n Bangladesh, the zoonotic disease anthrax caused by Bacillus anthracis is enzootic in various districts of the country (1). For example, from 2008 to 2009 there were a total of 886 registered animal cases and between 18 August and 2 October 2010 alone, 607 human cases were reported (2). In May 2013 an outbreak among livestock occurred in Sadar (Dhaka division), a subdistrict of Tangail located in central Bangladesh as published in ProMED-mail (archive 20130517.1720541), where multiple animal cases are typically reported each year. In September 2013, a site from a cowshed housing several healthy cows was sampled and soil from 5 cm depth withdrawn for cultivation. Isolation of live B. anthracis was accomplished using the ground anthrax bacillus refined isolation (GABRI) method published previously (3). Strain Tangail-1 harbored both B. anthracis virulence plasmids pXO1 and pXO2 as confirmed by real-time PCR assays (4, 5). Genotyping based on canonical single-nucleotide polymorphism (canSNP) (6) grouped strain Tangail-1 into the A.Br.001/002 branch, which has previously been isolated in Bangladesh (2) and other South Asian countries including China (6, 7), and Central Europe (8, 9). Notably, this canSNP-group of B. anthracis seems to be predominant in Bangladesh (1, 2). Whole-genome shotgun (WGS) sequencing of B. anthracis Tangail-1 was performed by Ion Torrent sequencing technology (Ion Torrent Systems Inc., USA). For the WGS library, 1,705,145 reads with a total of 460 Mbases were generated. Bowtie-2 (10) was used for mapping to Ames Ancestor chromosome, plasmid pXO1 and pXO2 (NC_007530.2, NC_007322.2, AE017335.3), respectively. The G⫹C content was calculated using an in-house Python script. The total length of the genome shotgun sequence of B. anthracis Tangail-1 was 5,227,292 bp with a 105-fold coverage for the chromosome (197-fold for pXO1 and 130-fold for pXO2), and the mean G⫹C content was 35%. For initial annotation, assembled contigs were submitted to the RAST annotation pipeline (11, 12). The B. anthracis Tangail-1 draft genome encodes 5,720 putative coding sequences (CDS). Annotation identified 11 copies of genes
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for 16S rRNA, 5S rRNA, and 23S rRNA within the genome; 95 tRNA loci were identified. The B. anthracis Tangail-1 genome represents a reference genome of a B. anthracis strain of the A.Br.001/ 002-clade from Bangladesh for further country-wide genotype analysis. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. CP015777 (pXO1), CP015778 (pXO2), and CP015779 (chromosome). The versions described in this paper are the first versions. ACKNOWLEDGMENTS Thanks are due to Linda Dobrzykowski and Philipp Vette for skillful technical assistance. This work was supported by funds from the German Ministry of Defense (Sonderforschungsprojekt 25Z1-S-431214 to M.A.). Work in Bangladesh was supported by the Bangladesh Academy of Sciences under BAS-USDA Program in Agriculture and Life Sciences.
FUNDING INFORMATION This work, including the efforts of Markus Heinrich Antwerpen, was funded by German Ministry of Defense (25Z1-S-431214). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
REFERENCES 1. Rume FI, Affuso A, Serrecchia L, Rondinone V, Manzulli V, Campese E, Di Taranto P, Biswas PK, Ahsan CR, Yasmin M, Fasanella A, Hugh-Jones M. 2016. Genotype analysis of Bacillus anthracis strains circulating in Bangladesh. PLoS One 11:e0153548. http://dx.doi.org/ 10.1371/journal.pone.0153548. 2. Fasanella A, Garofolo G, Hossain MJ, Shamsuddin M, Blackburn JK, Hugh-Jones M. 2013. Bangladesh anthrax outbreaks are probably caused by contaminated livestock feed. Epidemiol Infect 141:1021–1028. http:// dx.doi.org/10.1017/S0950268812001227. 3. Fasanella A, Di Taranto P, Garofolo G, Colao V, Marino L, Buonavoglia D, Pedarra C, Adone R, Hugh-Jones M. 2013. Ground anthrax bacillus refined isolation (GABRI) method for analyzing environ-
Genome Announcements
genomea.asm.org 1
Rume et al.
4.
5.
6.
7.
mental samples with low levels of Bacillus anthracis contamination. BMC Microbiol 13:167. http://dx.doi.org/10.1186/1471-2180-13-167. Ellerbrok H, Nattermann H, Ozel M, Beutin L, Appel B, Pauli G. 2002. Rapid and sensitive identification of pathogenic and apathogenic bacillus anthracis by real-time PCR. FEMS Microbiol Lett 214:51–59. http:// dx.doi.org/10.1111/j.1574-6968.2002.tb11324.x. Antwerpen MH, Zimmermann P, Bewley K, Frangoulidis D, Meyer H. 2008. Real-time PCR system targeting a chromosomal marker specific for Bacillus anthracis. Mol Cell Probes 22:313–315. http://dx.doi.org/10.1016/ j.mcp.2008.06.001. Van Ert MN, Easterday WR, Huynh LY, Okinaka RT, Hugh-Jones ME, Ravel J, Zanecki SR, Pearson T, Simonson TS, U’Ren JM, Kachur SM, Leadem-Dougherty RR, Rhoton SD, Zinser G, Farlow J, Coker PR, Smith KL, Wang B, Kenefic LJ, Fraser-Liggett CM, Wagner DM, Keim P. 2007. Global genetic population structure of Bacillus anthracis. PLoS One 2:e461. http://dx.doi.org/10.1371/journal.pone.0000461. Li S, An X, Huang Y, Pei G, Cao D, Mi Z, Gu Z, Zhao X, Li J, Gu G, Tong Y. 2015. Source tracking of an anthrax outbreak in northeastern China using complete genome analysis and MLVA genotyping. Eur J Clin Microbiol Infect Dis 34:89 –100. http://dx.doi.org/10.1007/s10096-014 -2195-7.
2 genomea.asm.org
8. Antwerpen M, Elschner M, Gaede W, Schliephake A, Grass G, Tomaso H. 2016. Genome sequence of Bacillus anthracis strain Stendal, isolated from an anthrax outbreak in cattle in Germany. Genome Announc 4(2): e00219-16. http://dx.doi.org/10.1128/genomeA.00219-16. 9. Girault G, Blouin Y, Vergnaud G, Derzelle S. 2014. High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery. BMC Genomics 15:288. http://dx.doi.org/10.1186/1471-2164-15-288. 10. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with bowtie 2. Nat Methods 9:357–359. http://dx.doi.org/10.1038/nmeth.1923. 11. Beyer W, Bellan S, Eberle G, Ganz HH, Getz WM, Haumacher R, Hilss KA, Kilian W, Lazak J, Turner WC, Turnbull PC. 2012. Distribution and molecular evolution of Bacillus anthracis genotypes in Namibia. PLoS Negl Trop Dis 6:e1534. http://dx.doi.org/10.1371/journal.pntd.0001534. 12. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/ 1471-2164-9-75.
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